Background/Aims: Peroxisome proliferator-activated receptors-γ (PPAR-γ) and its co-activator-1α (PGC-1α) are involved in the regulation of lipid and glucose metabolisms. This study aimed to investigate the genetic polymorphisms of PPAR-γ and PGC-1α in Chinese people and their influence on plasma adiponectin levels and non-alcoholic fatty liver disease (NAFLD) susceptibility. Methods: Ninety-six patients with NAFLD and 96 healthy controls were included. The single nucleotide polymorphisms (SNPs) of C161T PPAR-γ and Gly482Ser PGC-1α genes were analysed by polymerase chain reaction and restriction fragment length polymorphism. Result: The CC, CT and TT genotypic distributions of the NAFLD group were significantly different from those of controls (55.2, 39.6, 5.2 vs. 74.0, 25.0, 1.0%; P = 0.015). The allelic frequencies of C and T were also different between the two groups (P = 0.004). As for the PGC-1α gene, there was no difference of the genotypic and allelic frequencies between the two groups (P>0.05). In NAFLD patients, the plasma adiponectin concentrations were lower in the PPAR-γ CT/TT genotypes compared with those in the CC genotype group (3.0±0.6 vs. 4.3±0.9, P = 0.02). Multivariate logistic regression analysis showed that CT/TT genotypes of PPAR-γ, TG, waist hip ratio, hypoadiponectinaemia and homoeostasis model assessment (HOMA)-IR were the risk factors for NAFLD. Conclusion: SNPs in the PPAR-γ, but not PGC-1α, gene are associated with NAFLD susceptibility possibly through the adiponectin pathway.